Furious iConverter is, as the name might suggest, a video conversion tool for use with iPod, iPod Nano, iPod Touch, iPhone, iPad.
The simple GTK interface provides users with a convenient front-end for converting any FFMpeg-supported video format into iPod/iPhone friendly MP4.

No set-up or configuration is required to use it, simple drag and drop your videos and hit the 'Start' button to convert. Video aspect ratio and quality is automatically automatically detected and converted accordingly.
Please help by reporting bugs/comments/suggestions

0.3.1.0
Added improved progress feedback, including total frames, current frames and estimated time remaining.
Fixed school boy error when determining video duration caused by incorrect calculation on the millisecinds to seconds.
Added support for libnotify
Changed the code which fetches total FPS to work with version of FFMPEG from medibuntu Natty repo

Version 0.2.0.0
Fixes Bug #625393
Changed to using h264 encoding over xvid

Version 0.1.1.0
Fixed Bug #616134 (Black bars aren’t really need on videos on the ipod and it seems to squish videos that start off at 4:3 or widescreen tv shows.)
Added an aspect ration preset for iPod Nano (Video)

Version 0.1.0.2
Added functionality to view the FFmpeg log on completion of the conversion process, if required. This facilitates bug tracking and investigation.

Version 0.1.0.1
Fixed a bug were the application would crash if a ‘Videos’ folder was not present in the user’s home directory. (Thanks to Jimcat for reporting this)

If you could email the contents of the folder /home/YOUR HOME/.furiusiconverter (where YOUR HOME is the name of your home folder) to marcus_furius@hotmail.com, I can take a look at the output.
I would suggest that you are missing the codec required for this kind of file as it is a proprietary video format from RealPlayer